M Beer

This study identifies SARAF as a repressor of the mild hypothermia response by regulating JUN and calcium dynamics, showing its role in cytoprotection against hypoxia.

This paper shows that astrocytes reprogram neuronal gene expression and chromatin accessibility, affecting thousands of genes and regulatory elements, including those linked to schizophrenia and Alzheimer's disease.

This study uses Perturb-seq to analyze how varying levels of pluripotency regulators affect hESC self-renewal and differentiation through single-cell RNA-seq.

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

The paper uses CRISPR-Cas9 screens to identify genes affecting stem cell fitness versus pluripotency identity, finding distinct and overlapping roles for chromatin and metabolic regulators.

The paper identifies conserved regulatory elements between humans and mice using a novel gapped-kmer alignment method, discovering 23,660 novel enhancers.

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

The paper uses a CRISPRi screen in hESC differentiation to identify enhancers with nonlinear regulatory activity, revealing a CTCF loop-constrained model for improved enhancer prediction.

Long-read sequencing of 81 human and mouse samples yields 200,000 full-length transcripts plus a triplet framework that separates promoter choice, splicing and 3' end use across tissues.

The paper reports 109 non-coding CRISPR screens analyzing 13.3Mb of the genome, identifies CRE-gene links, and provides guidelines and tools for screening non-coding regulatory elements.

This paper introduces a sequence-based method to correct barcode bias in MPRA experiments, improving detection of functional regulatory variants and capturing post-transcriptional regulatory features.

The paper introduces a mathematical model to predict CTCF-mediated chromatin loop formation and shows it accurately predicts ChIA-PET interaction data.

The paper shows that local epigenomic features cannot accurately distinguish interacting from non-interacting enhancer-promoter pairs due to overfitting in machine learning models.

The paper identifies Parkinson's risk variants in a SNCA enhancer by analyzing open chromatin in mouse dopamine neurons and validates their function in zebrafish and mice.

The paper identifies genetic variants affecting chromatin accessibility in T cells and links them to gene expression and autoimmune disease.

The paper identifies a critical genomic region on chromosome 19 that protects the active X chromosome from XIST-mediated silencing, linking its disruption to embryonic female loss.